Sequence‐dependent folding and unfolding of ligand‐bound purine riboswitches

Prychyna, Oksana; Dahabieh, Michael; O’Neill, Melanie A.

doi:10.1002/bip.21283

Cited by 15 publications

(21 citation statements)

References 59 publications

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“…Experimental studies have shown that binding of the ligand to the riboswitch leads to tightening and stabilization of the tertiary interactions between L2 and L3 2933; 35; 47 Hence, the two models of the apo forms of the riboswitch, A1 and A2 , developed in this study represent two extremes of the experimental regimen, with the results obtained from the individual simulations allowing for interpretation of the available experimental data.…”

Section: Resultsmentioning

confidence: 99%

Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch

Priyakumar

MacKerell

2010

Journal of Molecular Biology

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Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, molecular dynamics (MD) simulations were performed in both the presence and absence of the ligand. In the absence of ligand, structural deviations were observed in the J23 junction and the P1 stem. Destabilization of the P1 stem in the absence of ligand involves the loss of direct stabilizing interactions with the ligand, with additional contributions from the J23 junction region. The J23 junction of the riboswitch is found to be more flexible and the tertiary contacts among the junction regions are altered in the absence of the adenine ligand; results suggest that the adenine ligand associates and dissociates from the riboswitch in the vicinity of J23. Good agreement was obtained with the experimental data with the results indicating dynamic behavior of the adenine ligand on the nanosecond timescale to be associated with the dynamic behavior of hydrogen bonding with the riboswitch. Results also predict that direct interactions of the adenine ligand with U74 of the riboswitch are not essential for stable binding even though it is crucial for its recognition. The possibility of methodological artifacts and force field inaccuracies impacting the present observations was checked by additional MD simulations in the presence of 2,6-diaminopurine and in the crystal environment.

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Section: Resultsmentioning

confidence: 99%

Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch

Priyakumar

MacKerell

2010

Journal of Molecular Biology

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“…However, when docking is compromised, e.g. at low concentrations of Mg 2+ ions, ligand binding may not be sufficient to dock the aptamer structure, leading to an array of coexisting and partially docked ligand-bound states that differ in local and global tertiary structure as recently suggested by stopped-flow (54), sm-FRET (22) and ultra-fast time-resolved spectroscopy (36,37). In this context, funneling this ensemble of stiff-liganded states towards a tightly packed mRNA-ligand complex, resembling the X-ray structure (20), may require assistance from specifically trapped divalent metal ions along the docking pathway.…”

Section: Discussionmentioning

confidence: 99%

Single-molecule chemical denaturation of riboswitches

Dalgarno

Bordello

Morris

et al. 2013

Nucleic Acids Research

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To date, single-molecule RNA science has been developed almost exclusively around the effect of metal ions as folding promoters and stabilizers of the RNA structure. Here, we introduce a novel strategy that combines single-molecule Förster resonance energy transfer (FRET) and chemical denaturation to observe and manipulate RNA dynamics. We demonstrate that the competing interplay between metal ions and denaturant agents provides a platform to extract information that otherwise will remain hidden with current methods. Using the adenine-sensing riboswitch aptamer as a model, we provide strong evidence for a rate-limiting folding step of the aptamer domain being modulated through ligand binding, a feature that is important for regulation of the controlled gene. In the absence of ligand, the rate-determining step is dominated by the formation of long-range key tertiary contacts between peripheral stem-loop elements. In contrast, when the adenine ligand interacts with partially folded messenger RNAs, the aptamer requires specifically bound Mg2+ ions, as those observed in the crystal structure, to progress further towards the native form. Moreover, despite that the ligand-free and ligand-bound states are indistinguishable by FRET, their different stability against urea-induced denaturation allowed us to discriminate them, even when they coexist within a single FRET trajectory; a feature not accessible by existing methods.

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“…The folding of the aptamer domain has been investigated using a number of experimental techniques including NMR [57, 95, 96], smFRET [52, 56], chemical probing [51], fast fluorescence spectroscopy [97, 98], single molecule force extension spectroscopy [91, 99, 100], as well as molecular dynamics simulation [101-104]. While all of these techniques observe different aspects of the folding process, together they yield a reasonably consistent model of the folding process.…”

Section: Folding Of the Riboswitchmentioning

confidence: 99%

The purine riboswitch as a model system for exploring RNA biology and chemistry

Porter¹,

Marcano-Velázquez²,

Batey³

2014

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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Over the past decade the purine riboswitch, and in particular its nucleobase-binding aptamer domain, has emerged as an important model system for exploring various aspects of RNA structure and function. Its relatively small size, structural simplicity and readily observable activity enable application of a wide variety of experimental approaches towards the study of this RNA. These analyses have yielded important insights into small molecule recognition, co-transcriptional folding and secondary structural switching, and conformational dynamics that serve as a paradigm for other RNAs. In this article, the current state of understanding of the purine riboswitch family is examined and how this growing knowledge base is starting to be exploited in the creation of novel RNA devices.

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Sequence‐dependent folding and unfolding of ligand‐bound purine riboswitches

Cited by 15 publications

References 59 publications

Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch

Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch

Single-molecule chemical denaturation of riboswitches

The purine riboswitch as a model system for exploring RNA biology and chemistry

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